Solutions for Exercise 9

Replacing glutamine for arginine removes the possibility of the dual hydrogen bonding interaction observed between Arg 13 and Gua 3A, but in principle that kind of interaction could be restored by swapping adenine for guanine at position 3A. When that swap is performed, one observes that the DNA fragment and peptide need to be moved closer together to promote a reasonable hydrogen bonding interaction (Figure 9S.1). Perhaps the reason behind the swap of Asp 16 for Glu 16 is that the additional methylene group in Glu blocks the closer approach of the peptide to the DNA fragment.

Figure 9S.1 Model of the interaction between glutamine 13 and adenine at position 3A.

In reality, however, it turns out that glutamine at position 13 specifies a thymine base at position 3A. A possible explanation could be the vdW interaction shown in Figure 9S.2.

Figure 9S.2 Model of the interaction between glutamine 13 and thymine at position 3A.